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Description
When we updated RcppArmadillo recently to help package Matrix propagate a change, we encountered a small change in Armadillo made between the 11.2.0 and 11.2.3 releases that marked our previous and current release. A number of packages would now throw deprecation warnings as Armadillo upstream activated those.
CRAN of course frowns on this so we temporarily disabled the warning in RcppArmadillo. Going forward we should aim to patch this in all affected packages, and we will try to provide PRs. This affects these packages:
- ACEt (athttps://r-forge.r-project.org/R/?group_id=2167) (patch created, tested and emailed 2022-09-01) (heard back 2022-09-04: "within a few weeks") (version 1.8.2 on CRAN 2022-09-26)
- autostsm (athttps://bitbucket.org/ajhubb/autostsm.git) (pull request made 2022-09-01) (version 3.0.2 at CRAN)
- BAMBI (athttps://github.com/c7rishi/BAMBI/) (alreadyaddressed by upstream) (version 2.3.4 on CRAN)
- BayesPPD (no known repo) (patch created, tested, and emailed 2022-09-04) (version 1.1.0 on CRAN 2022-11-12) (new patch emailed 2023-01-15, email reply 2023-05-11, fixed on CRAN 2023-05-09 (!!))
- BNPMIXcluster (athttps://github.com/chriscarmona/BNPMIXcluster)
(PR created 2022-09-04) (merged 2022-09-09) (no longer on CRAN as of 2022-11-20) - cccp (athttps://github.com/bpfaff/cccp) (PR created 2022-09-04) (merged 2022-09-06) (version 0.2-9 on CRAN 2022-09-09) (SecondPR created 2023-01-15) (new version on CRAN 2023-12-09)
- finity (athttps://github.com/x0range/finity) (PR created 2022-09-05) (merged 2023-11-19) (new version 0.1.5 on CRAN 2023-12-20)
- greed (athttps://github.com/comeetie/greed) (PR created 2022-09-05) (heard back 2022-09-06 'within days') (merged 2022-09-07) (version 0.6.1 on CRAN 2022-10-03)
- gren (athttps://github.com/magnusmunch/gren) (PR created 2023-01-15 for updated
insert_rows()signature) (no longer on CRAN as of 2023-12-07) - grove (athttps://github.com/jacsor/grove) (PR created 2022-09-05) (new version on CRAN 2023-12-10)
- growfunctions (no known repo) (patch for updated
insert_rows()signature created, tested and emailed 2023-01-15) (new version on CRAN 2023-12-12) - handwriter (athttps://github.com/CSAFE-ISU/handwriter) (PR created 2022-09-06) (merged 2022-09-09) (see this issue dated 2023-01-11 aboutpossible maintainer transition) (new version 2.0.2 on CRAN 2023-10-13, got heads-up 2023-10-20) (new version on CRAN 2023-12-07)
- HARModel (athttps://github.com/emilsjoerup/HARModel) (PR created 2022-09-07) (merged 2023-01-08) (stated 2023-01-09 that package willnot get updated at CRAN) (off CRAN as of 2023-12-19)
- mdgc (athttps://github.com/boennecd/mdgc) (PR create 2022-09-08) (merged 2022-09-08) (version 0.1.6 on CRAN 2022-09-10)
- minimaxdesign (no known repo) (patch created, tested and emailed 2022-09-10) (heard back 2022-09-12, "in the coming months") (no longer on CRAN as of 2024-01-12)
- MRS (athttps://github.com/jacsor/MRS) (PR created 2022-09-10) (merged 2022-10-07) (new version on CRAN 2023-12-09)
- nlmixr (athttps://github.com/nlmixrdevelopment/nlmixr) (PR created 2022-09-10) (no longer on CRAN as of 2022-10-10)
- nlmixr2est (athttps://github.com/nlmixr2/nlmixr2est) (fix created andmerged by upstream 2022-09-01) (new version 2.1.0 on CRAN 2022-10-22)
- pedmod (athttps://github.com/boennecd/pedmod) (committed upstream 2022-09-08) (new version 0.2.4 on CRAN 2022-09-11)
- robustHD (athttps://github.com/aalfons/robustHD) (PR created 2023-01-15 for updated
insert_rows()signature) (merged 2023-01-18) (version 0.7.4 on CRAN 2023-01-18) - smog (athttps://github.com/chongma8903/smog) (PR made 2022-09-11) (merged 2022-09-12) (no longer on CRAN as of 2024-01-12)
- SparseFactorAnalysis (no known repo) (patch created, tested and emailed 2022-09-12) (no longer on CRAN as of 2024-01-12)
- spBFA (athttps://github.com/berchuck/spBFA) (committed upstream 2022-09-04, on CRAN as 1.2, 2022-09-04)
- spCP (athttps://github.com/berchuck/spCP) (committed upstream 2022-09-04, on CRAN as 1.3, 2022-09-05)
- specs (athttps://github.com/wijler/specs) (PR made 2022-09-12) (no longer on CRAN as of 2023-12-07)
- TreeBUGS (athttps://github.com/danheck/TreeBUGS) (heard back from upstream 2022-09-06, "at CRAN in 1.4.9")
- UComp (athttps://github.com/djpedregal/UComp) (PR made 2022-09-13) (no longer on CRAN as of 2023-01-24)
- womblR (athttps://github.com/berchuck/womblR) (committed upstream 2022-09-04, on CRAN as 1.0.5, 2022-09-05)
- bayesm (no known repo) (detected in re-run 2023-09-16) (patch emailed 2023-09-20) (incorporated upstream 2023-09-22) (on CRAN as 3.1-6 on 2023-09-23)
- ordinalClust (no known repo) (detected in re-run 2023-09-16) (patch emailed 2023-09-20) (no longer on CRAN as of 2024-01-12)
- mixedClust (no known repo) (deteced in re-run 2023-10-29) (patch email 2023-10-31) (no longer on CRAN as of 2024-01-12)
The full log from the CRAN check (before we amended the now-uploaded version 0.11.2.3.1 to no flag deprecation) follows
Details
Changes to worse in reverse depends:Package: ACEtCheck: whether package can be installedNew result: WARNING Found the following significant warnings: AtCtEt.cpp:87:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEt.cpp:88:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEt.cpp:122:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEt.cpp:123:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEt.cpp:198:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEt.cpp:199:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEt.cpp:262:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEt.cpp:263:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEt.cpp:395:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEt.cpp:396:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEt.cpp:429:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEt.cpp:430:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:108:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:109:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:142:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:143:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:345:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:346:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:374:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:375:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:461:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:462:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:507:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:508:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:644:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:645:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:678:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtCtEtp.cpp:679:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:84:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:85:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:111:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:112:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:251:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:252:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:272:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:273:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:337:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:338:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:367:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:368:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:468:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:469:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:494:35: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] AtEtp.cpp:495:35: warning: ‘arma::mat_injector<arma::Row<eT> > arma::Row<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]Package: autostsmCheck: whether package can be installedNew result: WARNING Found the following significant warnings: kalmanfilter.cpp:108:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations]Package: BAMBICheck: whether package can be installedNew result: WARNING Found the following significant warnings: vmcos_llik_grad.cpp:185:28: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] vmcos_llik_grad.cpp:212:54: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] vmsin_llik_grad.cpp:154:21: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] vmsin_llik_grad.cpp:163:21: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] vmsin_llik_grad.cpp:473:10: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]Package: BayesPPDCheck: whether package can be installedNew result: WARNING Found the following significant warnings: PP_fixed_glm.cpp:98:12: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] PP_random_glm.cpp:96:10: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations]Package: BNPMIXclusterCheck: whether package can be installedNew result: WARNING Found the following significant warnings: get_latents.cpp:44:19: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]Package: cccpCheck: whether package can be installedNew result: WARNING Found the following significant warnings: DCP.cpp:409:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] DLP.cpp:470:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] DNL.cpp:317:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] DQP.cpp:340:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] GPP.cpp:276:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] RPP.cpp:225:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]Package: finityCheck: whether package can be installedNew result: WARNING Found the following significant warnings: finite_moment_test.cpp:412:22: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]Package: greedCheck: whether package can be installedNew result: WARNING Found the following significant warnings: DcSbm.cpp:210:9: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] DcSbm.cpp:212:10: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] DcSbmUndirected.cpp:91:9: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] DcSbmUndirected.cpp:93:10: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] MultSbm.cpp:198:9: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] MultSbm.cpp:200:10: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] MultSbmUndirected.cpp:77:9: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] MultSbmUndirected.cpp:79:10: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] Sbm.cpp:153:9: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] Sbm.cpp:155:10: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] SbmUndirected.cpp:63:9: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] SbmUndirected.cpp:65:10: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations]Package: groveCheck: whether package can be installedNew result: WARNING Found the following significant warnings: hmg.cpp:202:25: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] hmg.cpp:203:40: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] hmg.cpp:453:33: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]Package: handwriterCheck: whether package can be installedNew result: WARNING Found the following significant warnings: CleanBinaryImage.cpp:265:23: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] ThinImageCpp.cpp:113:32: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] ThinImageCpp.cpp:207:30: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] ThinImageCpp.cpp:220:32: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] ThinImageCpp.cpp:233:32: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] ThinImageCpp.cpp:246:32: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] ThinImageCpp.cpp:261:32: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] ThinImageCpp.cpp:280:27: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]Package: HARModelCheck: whether package can be installedNew result: WARNING Found the following significant warnings: HARDataCreationC.cpp:43:31: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]Package: mdgcCheck: whether package can be installedNew result: WARNING Found the following significant warnings: test-pmvnorm.cpp:40:15: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-pmvnorm.cpp:41:14: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-pmvnorm.cpp:42:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-pmvnorm.cpp:44:14: warning: ‘arma::mat_injector<arma::Mat<eT> > arma::Mat<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:33:14: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:35:14: warning: ‘arma::mat_injector<arma::Mat<eT> > arma::Mat<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:91:15: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:92:14: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:93:15: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:95:14: warning: ‘arma::mat_injector<arma::Mat<eT> > arma::Mat<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:141:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:142:12: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:143:15: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:203:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:204:12: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:205:15: warning: ‘arma::mat_injector<arma::Mat<eT> > arma::Mat<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:292:14: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:294:14: warning: ‘arma::mat_injector<arma::Mat<eT> > arma::Mat<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:301:15: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:374:15: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:375:14: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:376:14: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:378:14: warning: ‘arma::mat_injector<arma::Mat<eT> > arma::Mat<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-restrict-cdf.cpp:385:15: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]Package: minimaxdesignCheck: whether package can be installedNew result: WARNING Found the following significant warnings: subfunc.cpp:322:20: warning: ‘arma::mat_injector<arma::Mat<eT> > arma::Mat<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]Package: MRSCheck: whether package can be installedNew result: WARNING Found the following significant warnings: main.cpp:41:34: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] recursion.cpp:645:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]Package: nlmixrCheck: whether package can be installedNew result: WARNING Found the following significant warnings: saem.cpp:746:51: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]Package: nlmixr2estCheck: whether package can be installedNew result: WARNING Found the following significant warnings: saem.cpp:948:51: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]Package: pedmodCheck: whether package can be installedNew result: WARNING Found the following significant warnings: test-cdfaprx.cpp:319:15: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:320:14: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:321:15: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:323:14: warning: ‘arma::mat_injector<arma::Mat<eT> > arma::Mat<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:471:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:472:12: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:473:15: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:544:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:545:12: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:614:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:615:12: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:616:15: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:617:11: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:620:11: warning: ‘arma::mat_injector<arma::Mat<eT> > arma::Mat<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:745:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:746:12: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:747:15: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:748:11: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:751:11: warning: ‘arma::mat_injector<arma::Mat<eT> > arma::Mat<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] test-cdfaprx.cpp:752:11: warning: ‘arma::mat_injector<arma::Mat<eT> > arma::Mat<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]Package: smogCheck: whether package can be installedNew result: WARNING Found the following significant warnings: glog.cpp:151:10: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] glog.cpp:253:10: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] glog.cpp:286:15: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] glog.cpp:320:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] glog.cpp:369:10: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations]Package: SparseFactorAnalysisCheck: whether package can be installedNew result: WARNING Found the following significant warnings: grad_est.cpp:33:19: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] grad_est.cpp:98:19: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] grad_est.cpp:116:10: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] grad_est.cpp:133:19: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] grad_est.cpp:160:20: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] hmc4sfa.cpp:45:14: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] test_gamma_pois.cpp:30:13: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]Package: spBFACheck: whether package can be installedNew result: WARNING Found the following significant warnings: DIAG_GetLogLik.cpp:51:19: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] DIAG_SamplePPD.cpp:37:19: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] PRED_EtaKrigging.cpp:33:19: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] PRED_YKrigging.cpp:33:19: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]Package: spCPCheck: whether package can be installedNew result: WARNING Found the following significant warnings: DIAG_NormalLogLik.cpp:30:17: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] DIAG_ProbitLogLik.cpp:30:17: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] DIAG_SamplePPD.cpp:40:17: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] DIAG_TobitLogLik.cpp:30:17: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] PRED_PredictFuture.cpp:33:17: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]Package: specsCheck: whether package can be installedNew result: WARNING Found the following significant warnings: specs.cpp:43:23: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]Package: TreeBUGSCheck: whether package can be installedNew result: WARNING Found the following significant warnings: betaMPT.cpp:51:9: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] betaMPT.cpp:76:9: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]Package: UCompCheck: whether package can be installedNew result: WARNING Found the following significant warnings: SSpace.h:1214:16: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] SSpace.h:1216:16: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations] SSpace.h:1218:12: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = unsigned int]’ is deprecated [-Wdeprecated-declarations]Package: womblRCheck: whether package can be installedNew result: WARNING Found the following significant warnings: DIAG_NormalLogLik.cpp:30:17: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] DIAG_SamplePPD.cpp:34:17: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] DIAG_TobitLogLik.cpp:29:17: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] PRED_ThetaKrigging.cpp:36:17: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations] PRED_YKrigging.cpp:28:17: warning: ‘arma::mat_injector<arma::Col<eT> > arma::Col<eT>::operator<<(eT) [with eT = double]’ is deprecated [-Wdeprecated-declarations]I have not looked at every one of these in detail but it seems thatmost if not all are from the change inArmadillo which deprecated the long-used form of initialization via<< (which we turned offunconditionally in the most recent CRAN release). What is in the mainline here now (soinstall_github() works), and can also be installed from thedrat repo viainstall.packages("RcppArmadillo", repos=c("https://RcppCore.github.io/drat")) has a conditional toggle which a) defaults to no deprecation for now to permit CRAN use and b) permits to re-enable deprecation to test your code. The code in the next 'detail' snippet has a minimal example. You need the newer RcppArmadillo from this repo or the drat to make it work.
Details
// keep uncommented to see the effect, or comment our for silence#defineRCPPARMADILLO_FORCE_NO_DEPRECATE1#include<RcppArmadillo.h>// [[Rcpp::depends(RcppArmadillo)]]constexprdouble alpha =1.23;// mock variables and valuesconstexprdouble beta =4.56;// [[Rcpp::export]]arma::vecoldCode() { arma::vecres(2); res << alpha << beta;// deprecated OLD initializationreturn(res);}// [[Rcpp::export]]arma::vecnewCode() { arma::vecres({ alpha, beta });// new standard modern C++ brace initializationreturn(res);}/*** Rstopifnot(packageVersion("RcppArmadillo") >= "0.11.2.3.1.1")oldCode()newCode()*/
You see the difference betweeboldCode() andnewCode(): initialization by<< (which Conrad wants to deprecate, but which we still allow to not get your package at CRAN) and initialization by the newer and preferred brace initialization common since C++11.
ChangeLog:
- maintainers emailed 2022-09-01 with initial story
- maintainers emailed 2022-09-02 re fix on define
- patches or PRs to all remaining packages made by 2022-09-13 (while several packages were already updated by their maintainers -- thank you!)